Neglected Truth
by Indifferent Infatuation
Summary: !HUMANISED! When yet another of Kowalski's inventions goes wrong, it unveils a secret that he had kept hidden for years and now with it out in the open, can his friends ever see him in the same way again? (Currently being reworked)
1. Chapter 1

It was midnight, or perhaps one o'clock or even two. He had no idea how long he'd spent dithering and staring up at the ceiling, wondering whether or not to go through with his plan or not. The exact time didn't matter, it was dark and more importantly, the other three were still asleep. He'd made sure to check several times before leaving the room. It was one of the disadvantages of sharing a room with his teammates; it was very difficult to slip away undetected, as each had learned the hard way.

Kowalski slowly descended the stairs, pausing every time they creaked, which was a lot. It took ten long minutes until he was in the basement. He flicked the light switch and was momentarily blinded by the sudden brightness. Once his eyes had adjusted to the light, he walked quickly to the iron door and tapped in a code on a nearby electric keypad. The door opened, revealing an elevator which he stepped inside and pressed a blue button.

A short while after pressing the button, the doors opened again and he walked out into his lab that was filled with odd bits of machinery that only he understood the purpose to. A work bench was covered in small, half finished inventions that he had put on hold in order to work on his creation that he felt most important. He typed in another code to open a door and turned on all the lights. The large room contained several finished inventions waiting to be tested, many of which couldn't be due to needing test subjects and he was less than willing to use himself after previous incidents.

In the centre of the room was something that could only be described as a rather big ray gun mounted on a tripod. It had a control panel that stuck out on a bendable arm. First, he walked over to the floor length mirror situated on one wall. Kowalski looked at himself, pushing his glasses up the bridge of his nose and running a hand through his dark brown hair, wondering if it had always been so long.

He was so busy looking at himself that he didn't hear the distant sound of a door opening and the elevator descending. It was only when the door to the room he was in opened that he realised someone had noticed he had tried to be stealthy about what he was doing. He froze in the position he was in; a hand on one hip and sticking his chest out.

"Skipper, Private, Rico, what are you three doing up?" Kowalski asked and smiled nervously.

Skipper scowled, "we could ask you the same question. Care to explain?"

"I-I couldn't sleep." Kowalski turned around to look at the three and put his arms behind his back. The look on Skipper's face told him that the answer he'd given wasn't sufficient. "So I thought I'd catch up on my latest projects."

"Well that's not so bad, is it Skipper?" Private rubbed his eyes sleepily and yawned.

"That still doesn't explain why you were looking at yourself in the mirror like an insecure teenage girl." Skipper folded his arms and glanced in the direction Kowalski was looking, "so if you are going to do some late night science, how about demonstrating that?" He jerked his thumb towards the machine in the middle of the room.

"It's not ready yet." Kowalski said hurriedly.

"Then why is it in your testing room?" Private asked curiously, not understanding exactly what was going on.

"W-well I can't test it now as it requires some setup." Kowalski rubbed the back of his neck, desperate to get out of the situation.

"We'll help." Rico said.

Kowalski's nervous smile dropped from his face, "oh no, you really don't have to. I need to run some preliminary tests first anyway, to make sure it's safe."

"What does it do?" Private stumbled over to it and Kowalski quickly stood in his way.

"That's not important." Kowalski stretched his arms out wide as if he were trying to hide the machine.

"Answer the private's question Kowalski. That's an order." Skipper demanded seriously. Kowalski chewed his lower lip anxiously and looked over his shoulder. Skipper sighed and pushed him out of the way and pulled the control panel closer to him and was about to read the words on it but Kowalski slammed his hand on it and tried to pull it away from his leader.

"Skipper you really don't want to do that." Kowalski attempted to power the machine down but Skipper shoved him aside and pressed "cancel" repeatedly.

"Kowalski, I don't want to have to use force against you." Skipper yelled as both struggled to have the control panel. Private and Rico watched, unsure of whether or not to intervene but Private was too scared to step in and Rico was enjoying watching the fight too much. Both slammed their closed fists down on the screen and as it began to flash red Kowalski stepped on Skipper's foot and elbowed him away to read the message flashing on the screen.

"No, no, no, this can't happen!" Kowalski pressed buttons frantically. Rico saw that Skipper was about to try and take the panel back and restrained him, pinning his arms behind his back. Private rushed to Kowalski's side in case he could help in anyway. "Duck!" Kowalski shouted and shoved Private to the floor and then lay on the floor himself. Rico followed in the same way and the machine exploded.

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><p>Skipper didn't know how much time had passed from the explosion to him regaining consciousness, all he knew was he had a headache and was covered in debris. His vision was blurry as he opened his eyes, and his headache grew worse as he sat upright.<p>

"Kowalski, what happened?" He asked. His voice sounded different. It was higher pitched and more feminine. He looked down at himself, and his suspicions were close to being confirmed. "Kowalski!" He yelled again but only succeeded in waking Private and Rico.

"Ow, my head really hurts." Private complained. He looked over at Skipper and his eyes widened. "What happened to you?" He crawled across the floor so that he was closer to his leader.

"Same thing that happened to you and Rico and I'm guessing Kowalski as well." Skipper wondered if Private hadn't actually noticed the changes that had happened to him, or was more concerned with Skipper than himself.

"Huh? Oh my goodness!" Private exclaimed as looked down and heard his voice properly. Private sounded young normally, but with his more female voice, he sounded like he was barely a teenager. He clasped his hands over his mouth and made the mistake of looking over at Rico who was far too enthusiastic about his new body.

Eventually, Kowalski woke up too and was immediately interrogated by Skipper, who asked him, "Kowalski, what has that invention of yours done to us?" He started calmly, and ended shouting.

"Well. It would appear that my invention has worked. It's reversed your biological sex. For all of us, actually." Kowalski explained and stared at his three teammates, dumbfounded.

"If that's what it's done, then why are you exactly the same?" Private questioned.

"That's a good point Private. Your voice is exactly the same and you don't have any of... these." Skipper gestured to his chest, inviting Kowalski to stare at it for which Skipper slapped him across the face for.

"Because I was a girl in the first place." Kowalski replied. Private gasped, Skipper glared at him and Rico raised one eyebrow and smiled.

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><p><strong>First I want to explicitly state that Kowalski is not transsexual in case you thought that, that's not something I would attempt because I don't think I'd be able to handle it well. This will be explained in the next few chapters but I wanted to make my previous point clear. Anyway, with that out of the way, I'm back! It was lovely to write this and it's also an insight into my personal headcanon. I hope you guys like reading it as much as I liked writing it.<strong>


	2. Chapter 2

The room fell silent and the three froze as they processed what Kowalski had just said. Eventually the silence was broken by Skipper laughing, as he presumed what his friend had said to be a joke. Private tittered nervously whilst Rico looked at the two of them, knowing that Kowalski wasn't one for telling jokes.

"Skipper, I'm afraid I'm not joking. I am, was, a girl." Kowalski confirmed it and Skipper and Private stopped laughing.

"So you've been lying to us the whole time we've known you?" Skipper looked to Rico and Private for support, and both looked equally as angry.

"No, I just neglected to tell the truth. It's an insignificant little detail anyway, why you should you be upset about it?" Kowalski avoided making eye contact.

"But why, Kowalski? And I would hardly call you secretly being a girl insignificant." Private asked.

"Well, when Skipper first phoned me up looking for someone new to join this team he was currently putting together, he kept saying how he needed a man, a guy for the job. What you were offering was exactly what I was looking for. Plus, I didn't think I'd be with you guys this long so I thought I wouldn't have to pretend for long." Kowalski explained. Skipper was not satisfied with his answer and stood up angrily so he could look down on Kowalski.

"You still could've told us. We wouldn't have treated you any differently." Skipper argued, putting his hands on his hips.

"Oh, really. Remember the time you were hypnotised into thinking you were a girl? You explicitly stated that a girl would be out of place doing what we do and you as good as quit until I had to get a DNA test done to prove to you, you were male." Kowalski stood up as well and folded his arms.

"So were you ever planning on telling us?" Skipper looked up at Kowalski.

"My whole reason for my invention was so that I never had to." Kowalski raised his voice and looked over at the pile of rubble that had once been his invention.

"If you'd just told us then you wouldn't have to make it!" Skipper shouted in response.

"And if you'd just kept out of my business then we wouldn't be in this situation!" Kowalski shouted back. Rico stood up and stood between them, placing a hand firmly on each of their chests, being careful where he put his hand on Skipper.

"Stop arguing." Rico said sternly.

"Fine. But Kowalski, you are officially suspended from all missions until you fix that damn machine and change us back. When you have done that you will be reinstated at the lowest rank possible. Even lower than private." Skipper told him.

"Understood. But I'm not going apologise because I'm not the one at fault here." Kowalski replied.

"If that's how you feel, then you can just stay down here 'til your job is done." Skipper turned on his heel and headed for the door, shortly followed by Private and Rico. When all three were out the door, Skipper locked it behind them and changed the password. Kowalski quickly realised this and pressed a button for the intercom next to the door.

"Skipper you can't just leave me down here." Kowalski said, starting to panic.

"Oh yes I can. Because that's what you want." Skipper replied over the intercom.

"Please don't. You know what happened last time I was left on my own." Kowalski hit his fist against the wall. There was no reply, no matter how much he pleaded. He slid down the wall, curled up in a ball and cried to himself.

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><p>Fifteen minutes later the door opened again and Kowalski looked up hopefully and thankfully, it was Private. "Skipper's calmed down now." Private told him with very little emotion in his voice.<p>

"Okay. Private, are you really angry with me? Did I really do something wrong?" Kowalski's voice was oddly high pitched, though that was mostly from the crying. He stood up and walked with Private out of the lab and into the elevator.

"Skipper's angry with you, and he says you've done something wrong." Private pressed the buttons for the elevator.

"Yes I know, but what do you think?" Kowalski urged him for a better answer. Private shrugged and tried to flatten his light brown hair as it was messed up from only just having gotten out of bed after failing to get back to sleep.

"I guess I'm not that angry with you lying to us. You did have a reason even if I don't quite understand it." Private looked around to make sure Skipper wasn't listening. They exited the elevator when the doors opened and then left the basement. When they got back to the bedroom, Skipper was waiting for them.

"You're not sleeping in the same room as us." Skipper said bluntly and slammed the door in Kowalski's face after allowing Private through. They did have a very large house, but only one proper bedroom, which was Skipper's doing to deter guests from trying to stay. In the end, Kowalski decided to sleep in the conservatory which did have sofas in it, not that they were very comfortable, but sleeping in the living meant he would possibly encounter one of the other three in the morning, something he wanted to avoid.

One positive thing about being in the conservatory was that he could look up at the stars during the night when he wasn't asleep. But it was slightly unnerving for him to know that the only thing separating him from whatever could be outside was glass. The clock that was on a shelf of a bookcase revealed the time to be three o'clock in the morning, the clock also highlighted how slowly time seemed to be moving with each tick of the hands. It also made him wonder why they didn't have a digital clock in there instead.

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><p><strong>Thanks for the reviewsfavourites/follows, they really encourage me to write quicker. Don't have much to say except, thanks for reading and constructive criticism is very welcome.**


	3. Chapter 3

Kowalski was awoken by the sound of glass smashing, followed by Private hurriedly saying that he'd clear it up. Momentarily forgetting about what had happened last night, Kowalski went to the kitchen where Private and Rico were cleaning up a bottle of milk that was in pieces on the floor.

"Need any help?" Kowalski offered but was politely declined. "Is Skipper awake yet?" He asked.

"No. Kowalski, if you don't mind me asking, how did you manage to keep it a secret?" Private asked as he mopped the milk up with a tea towel.

"Well, most of it is natural, the voice is the only thing that isn't. And that's done by a lot of practice. I used it for answering phones." Kowalski explained and pressed the pedal on the bin so Rico could put the shards of glass into it. Kowalski had to keep back a smile as he looked at the two of them who looked oddly cute in their clothes that were now too big for them.

In the quiet they heard the bedroom door creak open and then Skipper shouted, "What have you broken now?" He walked into the kitchen, wearing only his pyjama t-shirt that still covered him decently and running a hand through his black hair. He stopped walking when he saw Kowalski.

"I'll just get dressed." Kowalski said quickly and walked away.

"Skipper, don't you think you're being just a tad harsh on Kowalski?" Private sat down at the table and Skipper joined him while Rico remained standing.

"No, I don't. I know what I'm doing Private, trust me." Skipper replied, which promptly dismissed any further questions Private had. One rule he had always been taught was not to question his leader's methods, no matter how preposterous they were. Rico switched the coffee machine on before Skipper asked and then left the kitchen and went to the bedroom and knocked on the door.

Kowalski opened the door, his shirt half tucked into his trousers and his glasses were slightly lopsided. "Yes, can I help you?"

"You okay?" Rico asked. Kowalski noticed that Rico's voice had become a lot more pleasant sounding, but it still didn't stop him talking like he had a limited vocabulary, which he didn't, he just preferred talking in that way.

"Sure. I'm as okay as I can be in this situation." Kowalski replied. Rico raised one eyebrow, showing that he didn't believe him. "Alright, I'm lying." Rico rolled his eyes and walked away, leaving Kowalski confused. But he didn't have time to wonder as there was a knock at the door and he instinctively ran to answer it.

"Hi Kowalski." It was Marlene. She was holding a large box with both hands and tried to blow her reddish-brown hair out of her eyes, but failed to do so.

"Oh hi Marlene. What are you doing here?" He didn't mean to sound as annoyed with her being there as he did, but he was otherwise preoccupied.

"It's Saturday. I always come round on a Saturday." Marlene reminded him.

"Who is it?" Private asked from behind him.

"Who was that?" Marlene tried to look past him but he stayed in the way.

"Just one moment. Don't go away." Kowalski smiled nervously and closed the door gently. He walked to the kitchen and Private followed him. "Marlene's here. It's Saturday. What should I tell her?" He informed and asked Skipper.

"Why don't you just make up some lie?" Skipper replied. Kowalski huffed and went back to the door and opened it again.

"Sorry Marlene, come in. I have something to tell you." He moved aside so Marlene could walk through. She went to the kitchen and froze when she saw what she perceived to be three random women standing around in their pyjamas.

"What's going on here?" Marlene set the box down on the table.

"I had a machine that would reverse people's biological sex, and there was a minor accident with it. Trust me that these are Skipper, Private and Rico." Kowalski answered and Marlene relaxed.

"I guess that's not too bad. Though you three could do with some new clothes, those are way too big." She sat down and then had a sudden thought, "why didn't you change?"

"Well it's funny you should say that-" Skipper started to say, but was interrupted by Kowalski "accidently" knocking the coffee machine off the counter and scalding his arm with boiling water. He turned the cold water tap on full and then stuck his arm under it, splashing himself and Private who was standing next to him.

"Whoops." Kowalski said with a completely serious expression and dragged Private by the arm so they could change and Marlene hurried after them in case she was needed.

"Is your arm alright?" Private asked concernedly.

"What was Skipper about to say?" Marlene questioned suspiciously. Kowalski and Private exchanged glances and the former sighed.

"It's nothing. Sorry Marlene, I don't think this is a good time to be here." Kowalski told her, as politely as he could, to leave.

"Okay, I can see something's up. How about next week? I'll leave the box on the table, it's for you guys anyway." Marlene said, and left. Private turned his attention back to Kowalski and tried to inspect his arm as he took his shirt off.

"I'll be fine, stop worrying." Kowalski put his arm in the air so it was out of Private's reach. He still jumped to try and get hold of it, unsuccessfully. After a few minutes, Private got a chair out of the corner of the room, stood on it and grabbed Kowalski's arm who then lost his balance and fell backwards, pulling Private on top of him. Both laughed, until they heard Skipper's voice and quickly composed themselves and resumed getting dressed.

When Private and Kowalski were finished and went back to where Skipper and Rico were, the latter two had disapproving looks on their faces that were directed at Kowalski.

"Why don't we see what's in the box Marlene left us?" Private suggested to try and diffuse the tension, or at least to distract them. He carefully lifted the lid off it to reveal a cake inside, with "two years" written on it in icing. Around the circumference of the cake, also written in icing, were their names.

"Oh yeah, we've known Marlene two years." Skipper clicked his fingers.

"That was nice of her to make us a cake." Private commented. Kowalski took the opportunity while they were focussing on something else, to slip away to his lab to start repairing his invention. He looked at it, lying in pieces on the floor, sighed and started sorted out the pieces into what could be used again and what had been obliterated beyond use. Usually he loved doing this, but when his friends and career were on the line, it suddenly became less fun.

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><p><strong>Wow, I'm really pleased with all the attention this story is getting, thank you all. And for once I'm actually ahead on my chapters so you can expect the next one Monday. I'm trying to upload one chapter every two days but it may fluctuate depending on the circumstances. So thanks to everyone for reading and reviewing and following and favouriting.<strong>


	4. Chapter 4

After a while, sorting out the pieces became calming for Kowalski. He always knew he could count on science to be there for him. The only downside was that as he started to enjoy it, he did it a lot quicker and would then have to face the other three. When he did have all the pieces in two neat and separate piles, he moved all the useless pieces to one side and spread them out on the floor, trying to figure out if any of them fitted together. Jigsaw puzzles had been a favourite pastime of his during his school years as he lacked friends and was too quick to finish his homework. He just liked the way all the parts would fit together perfectly and nothing was out of place.

It was a few hours later when he finally realised how hungry he was and left his lab and went to the kitchen where a note had been left on the table for him. Kowalski could easily recognise the handwriting as Private's barely legible scrawls, in the note he hurriedly explained that he, Skipper and Rico, were out on a mission. Kowalski stayed still, holding the note in his hand and staring at it blankly. He didn't really think Skipper would carry out on his decision to suspend Kowalski from all team business. He put the note down, opened the freezer and took out a large tub of Private's strawberry ice cream, grabbed the largest spoon out of the cutlery drawer and started eating.

Halfway through the tub, the doorbell rang and Kowalski reluctantly got up to answer it. He had ice cream smeared across half his face and his red eyes gave away the fact that he'd spent half an hour crying into a tub of ice cream.

"Hello! Happy birthday!" Julien thrust a small parcel wrapped in newspaper into Kowalski's hand and smiled eagerly.

"It's not my birthday." Kowalski looked at the present confusedly, as did Julien.

"Mort, you told me it was the sciencey one's birthday." Julien turned his attention to Mort who was standing beside him, wearing a party hat with a chin strap and holding face painting supplies.

"Oopsie, I meant to say it was my birthday." Mort giggled. Julien pulled the chin strap on Mort's hat and then let go of it so it snapped hard to his chin.

"Well as we're here, how about a party?" Julien suggested excitedly and pushed Kowalski out of the way and walked inside the house, shortly followed by Mort.

"I'm not in the mood and I was in the middle of something, so can you please leave?" Kowalski held the door open for them to leave.

"Is that any way to address your king?" Julien asked and pointed to the crown he had on his head. He claimed to be king of Madagascar, but no one apart from Mort believed him.

"Just leave." Kowalski said in such a defeated tone that Julien and Mort knew that this was not a time for partying, and did as they said. Mort ran down the path leading to the gates of the house but Julien hung behind.

"Where are those other three?" Julien lingered in the doorway. Kowalski didn't bother replying, pushed him out the door and closed it. He then went and found Private's MP3 player and some speakers and walked back to the kitchen and started playing all the over the top sad songs he could find and finished off the ice cream, falling asleep afterwards.

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><p>A couple of hours later, the three returned from what started out as a mission and ended up as a shopping trip with Marlene whom they bumped into. Skipper and Private walked through the front door and saw Kowalski, asleep with his head in the ice cream tub. Rico soon followed them, carrying several shopping bags.<p>

"Should we wake him?" Private asked Skipper in a whisper.

"She's fine." Skipper replied and closed the door after Rico.

"She?" Private repeated, confused.

"Yes, she. Because that's what Kowalski is." Skipper said and went to living room. Private looked at Kowalski and then at Rico, who shook his head, so Private accompanied Skipper. Rico noticed that his laptop had been left in its bag leaning against one of the kitchen counters and took it out and sat opposite Kowalski at the dinner table. Whilst he was browsing the internet for images that amused him, Kowalski woke up.

"When did you get back?" Kowalski lifted his head up and readjusted his glasses, wiping the ice cream off them first. Rico shrugged his shoulders and glanced up, feeling pity for his friend. "I'll get back to what I was doing." Kowalski stood up to leave, but paused by the freezer and took another tub of ice cream and spoon. When he saw the look of disappointment on Rico's face, he grinned guiltily and hurried back to his lab.

"Oh god, not this garbage." Skipper complained as Private turned the television on and switched to his favourite programme; the Lunacorns.

"You said I could watch whatever I wanted. And the Lunacorns is a great show." Private set the television remote down on the end table next to him, out of Skipper's reach, and pulled his stuffed Lunacorn toy closer to him.

"It's for little girls, that's what it is." Skipper put his hands behind his head and his feet up on the coffee table.

"That doesn't mean I can't watch it." Private replied indignantly.

"Yeah, but I bet it's secretly brainwashing kids with all its bright colours and subliminal advertising. It's real, I tell you." Skipper's eyes darted around the room like he expected someone to be spying on them. He was only acting paranoid, but it was reassuring to Private that he was behaving like he usually did.

"It's just an innocent cartoon that can be enjoyed by people of all ages and gender." Private hugged his Lunacorn toy tightly as he tried to focus on the television.

"I can't take you seriously when you're holding that doll. I swear you're as bad as Rico was." Skipper shuddered at the memory of when he'd caught Rico playing with Barbie dolls. Thinking about it, Skipper would've been less surprised if it'd been Private or Rico who were secretly female, but still just as betrayed.

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><p><strong>I don't know exactly why I wrote the ice cream scene, but it amused me so I left it in. And just as a treat, I'm uploading this chapter a day early because of all the lovely reviewsfollows/favourites I've had. You guys are just awesome. And in case there was any confusion, the pairing for this story is Kowalski/Private which will be expanded upon in chapter six. Fun fact: the pairing originally meant for this story was Kowalski/Rico, but I thought there were enough of those out there already.**


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